The issue appears to be between Intel MPI and CUDA 3.2
The following env. variable solves the crash:
I_MPI_FABRICS=shm:ofa
On Tue, Aug 23, 2011 at 1:30 PM, Carlos P Sosa <cpsosa.msi.umn.edu> wrote:
>
>
> Hello,
>
> I just built PMEMD for GPGPUs according to (http://ambermd.org/gpus/), I
> used the Intel MPI version (intel/impi/4.0.1.007). Then I tested it with
> the standard jac benchmark without vlimit
>
> short md, jac, power 2 FFT
> &cntrl
> ntx=7, irest=1,
> ntc=2, ntf=2, tol=0.0000001,
> nstlim=1000,
> ntpr=5, ntwr=10,
> dt=0.001,
> cut=9.,
> ntt=0, temp0=300.,
> /
> &ewald
> nfft1=64,nfft2=64,nfft3=64,
> /
>
> Has anybody seen this problem? The build ends successfully. I am using
> PBS with 2 nodes. Did I forget any patches?
>
> [0:node037] rtc_register failed 196608 [0] error(0x30000): unknown error
>
> Assertion failed in file ../../dapl_module_send.c at line 4711: 0
> internal ABORT - process 0
> rank 0 in job 1 node037_43404 caused collective abort of all ranks
> exit status of rank 0: killed by signal 9
> ----------------------------------------
>
> Final step in the build:
>
> Leaving directory `/home/applications/AMBER/11/amber11/src/pmemd/src/cuda'
> mpif90 -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -o pmemd.cuda.MPI
> gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o
> mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o
> dynamics_dat.o img.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o
> pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o
> pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o
> nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o
> dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o
> runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o
> timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o
> random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
> master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o
> gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o
> cmap.o charmm.o charmm_gold.o -L/usr/local/cuda-3.2/lib64
> -L/usr/local/cuda-3.2/lib -lcufft -lcudart ./cuda/cuda.a
> /home/cpsosa/applications/AMBER/11/amber11/lib/libnetcdf.a
> make[2]: Leaving directory
> `/home/applications/AMBER/11/amber11/src/pmemd/src'
> Installation of pmemd.cuda.MPI complete
> make[1]: Leaving directory `/home/applications/AMBER/11/amber11/src/pmemd'
>
> Thanks
>
> Carlos P Sosa
> Biomedical Informatics and Computational Biology (BICB) Consultant
> Minnesota Supercomputing Institute
> for Advanced Computational Research
> University of Minnesota
> Walter Library 509
> 117 Pleasant Street
> Minneapolis, MN 55455
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Carlos P Sosa, Ph.D.
Biomedical Informatics and Computational Biology (BICB) Consultant
Minnesota Supercomputing Institute
for Advanced Computational Research
University of Minnesota
Walter Library 509
117 Pleasant Street
Minneapolis, MN 55455
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Received on Wed Aug 24 2011 - 14:30:02 PDT
